As the technology of sensor and actuator production has rapidly developed in recent years and the computation power of embedded processors has increased, unmanned aerial vehicles (UAVs) have become attractive means of testing complex control algorithms. Apart from the development of new control control algorithms, it is crucial how they can be implemented and tested on the target platforms before flights. This article presents two methods that are suitable for rapid prototype design, test and efficient code generation. One of them provides a graphical interface and automatic code generation, which reduces me time required to develop a control algorithm. The other makes use of a highly configurable real-time operating system specially designed for embedded systems. The two approaches are illustrated by case studies, namely, the implementation of the control system of an autonomous aeroplane and a quadrotor helicopter.